Fail during calculation of mutation events

[phiweger]

Same error as in #10 :

# These both fail, version is v1.0:
snppar -t timetree.nwk -m core.aln -l 4snppar.positions.txt -g target.gbk
snppar -s 4snppar.csv -t timetree.nwk -g target.gbk

Symmetrized rates from j->i (W_ij):
	A	C	G	T	-
  A	0	0.9229	0.7454	0.418	62.7575
  C	0.9229	0	0.5651	0.5147	46.3287
  G	0.7454	0.5651	0	0.932	48.9164
  T	0.418	0.5147	0.932	0	54.4489
  -	62.7575	46.3287	48.9164	54.4489	0

Actual rates from j->i (Q_ij):
	A	C	G	T	-
  A	0	0.1267	0.1024	0.0574	8.6174
  C	0.2632	0	0.1612	0.1468	13.2122
  G	0.2639	0.2	0	0.3299	17.317
  T	0.0893	0.1099	0.1991	0	11.6294
  -	0.6218	0.459	0.4847	0.5395	0


--- alignment including ancestral nodes saved as
	 treetime_out/ancestral_sequences.fasta

--- tree saved in nexus format as
	 treetime_out/annotated_tree.nexus



Extracting mutation events from ASR results...
Traceback (most recent call last):
  File ".../bin/snppar", line 8, in <module>
    sys.exit(main())
  File ".../bin/snppar.py", line 2648, in main
    snps_mapped, mapped_node_sequences, node_names_mapped = mapSNPsTT(snps_to_map,snptable,strains,arguments.tree,directory,tree,prefix,log)
  File ".../bin/snppar.py", line 1326, in mapSNPsTT
    snps_mapped = readMappedSNPs(output_dir+'annotated_tree.nexus',tree,snps_to_map,snptable)
  File ".../bin/snppar.py", line 2524, in readMappedSNPs
    derived_node = the_tree.search_nodes(name=parts[0])[0]
IndexError: list index out of range

As input I use a tree and SNP alignment where the reference sequence, to which target.gbk corresponds, has been removed from the alignment and tree. Is that a problem?